The Plant Genome Integrative Explorer Resource: PlantGenIE.org. Sundell, D., Mannapperuma, C., Netotea, S., Delhomme, N., Lin, Y. C., Sjodin, A., Van de Peer, Y., Jansson, S., Hvidsten, T. R., & Street, N. R. New Phytol, 208(4):1149–56, December, 2015. Edition: 2015/07/21![The Plant Genome Integrative Explorer Resource: PlantGenIE.org [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.
@article{sundell_plant_2015,
title = {The {Plant} {Genome} {Integrative} {Explorer} {Resource}: {PlantGenIE}.org},
volume = {208},
issn = {1469-8137 (Electronic) 0028-646X (Linking)},
shorttitle = {The {Plant} {Genome} {Integrative} {Explorer} {Resource}},
url = {https://www.ncbi.nlm.nih.gov/pubmed/26192091},
doi = {10.1111/nph.13557},
abstract = {Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.},
language = {en},
number = {4},
urldate = {2021-06-07},
journal = {New Phytol},
author = {Sundell, D. and Mannapperuma, C. and Netotea, S. and Delhomme, N. and Lin, Y. C. and Sjodin, A. and Van de Peer, Y. and Jansson, S. and Hvidsten, T. R. and Street, N. R.},
month = dec,
year = {2015},
note = {Edition: 2015/07/21},
keywords = {*Databases, Factual, *Genes, Plant, *Genome, Plant, Arabidopsis/*genetics, Computational Biology, Forests, Gene Expression, Genomics/methods, Internet, Models, Biological, Populus, Populus/*genetics, RNA, Plant, Sequence Analysis, DNA, Tracheophyta/*genetics, Trees/*genetics, annotation, coexpression, conifer, database, genome browser, transcriptomics, web resource},
pages = {1149--56},
}
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